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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
| author | drosofff |
|---|---|
| date | Tue, 06 Dec 2016 17:29:34 -0500 |
| parents | a006d42dd759 |
| children | 0bd777f0d6d8 |
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<tool id="lumpy" name="lumpy-sv" version="0.2"> <description>find structural variants</description> <requirements> <requirement type="package" version="0.2.12">lumpy-sv</requirement> <requirement type="package" version="1.3.1">samtools</requirement> <requirement type="package" version="1.11.2">numpy</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <version_command>lumpy --version</version_command> <command><![CDATA[ #if $analysis_type.analysis_type_list == "one_sample": ln -f -s $analysis_type.input_file input.bam && #else: ln -f -s $analysis_type.input_file input.A.bam && ln -f -s $analysis_type.input_fileB input.B.bam && #end if #if $analysis_type.analysis_type_list == "one_sample": #if $seq_method.seq_method_list == "paired-end": samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" && samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && samtools sort input.discordants.unsorted.bam > input.discordants.bam && samtools sort input.splitters.unsorted.bam > input.splitters.bam && samtools view -r readgroup input.bam |tail -n +$seq_method.additional_params.samplingValue |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$seq_method.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.discordants.bam $discordants && mv input.splitters.bam $splits && mv input.lib.histo $histogram && mv output.vcf $vcf_call && rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt #end if #if $seq_method.seq_method_list == "single-read": samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.splitters.unsorted.bam $splits && mv output.vcf $vcf_call #end if #else: #if $seq_method.seq_method_list == "paired-end": samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" && samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" && samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" && samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam && samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam && samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam && samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam && samtools view -r readgroup input.A.bam |tail -n +$seq_method.additional_params.samplingValue |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt && samtools view -r readgroup input.B.bam |tail -n +$seq_method.additional_params.samplingValue |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$seq_method.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$seq_method.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.A.discordants.bam $discordants && mv input.B.discordants.bam $discordantsB && mv input.A.splitters.bam $splits && mv input.B.splitters.bam $splitsB && mv input.A.lib.histo $histogram && mv input.B.lib.histo $histogramB && mv output.vcf $vcf_call && rm input.A.discordants.unsorted.bam input.B.discordants.unsorted.bam input.A.splitters.unsorted.bam input.B.splitters.unsorted.bam meandevA.txt meandevB.txt #end if #if $seq_method.seq_method_list == "single-read": samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" && samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" && lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf && mv input.A.splitters.unsorted.bam $splits && mv input.B.splitters.unsorted.bam $splitsB && mv output.vcf $vcf_call #end if #end if ]]></command> <!-- basic error handling --> <inputs> <conditional name="analysis_type"> <param help="Single or paired conditions (eg tumor vs normal)" label="Analysis type" name="analysis_type_list" type="select"> <option selected="True" value="one_sample">One Sample</option> <option value="two_sample">Two samples</option> </param> <when value="one_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> </when> <when value="two_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/> </when> </conditional> <conditional name="seq_method"> <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> <option selected="True" value="paired-end">Paired-end sequencing</option> <option value="single-read">Single-read sequencing</option> </param> <when value="paired-end"> <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> <section name="additional_params" title="Additional Options" expanded="False"> <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" /> <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" /> <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" /> <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> </section> </when> <when value="single-read"> <section name="additional_params" title="Additional Options" expanded="False"> <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> </section> </when> </conditional> </inputs> <outputs> <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="vcf" name="vcf_call" type="data" label="Lumpy Variant Calling (vcf format)"/> </outputs> <tests> <test> <param name="analysis_type" value="one_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> <param name="mw" value="4"/> <param name="tt" value="0"/> <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output.vcf" ftype="vcf"/> </test> </tests> <help> **lumpy-sv manual** Read the lumpy-sv_ documentation for details on using lumpy. .. _lumpy-sv: https://github.com/arq5x/lumpy-sv **lumpy options** v 0.2.13 Author: Ryan Layer (rl6sf@virginia.edu) Summary: Find structural variations in various signals. Options:: -g Genome file (defines chromosome order) -e Show evidence for each call -w File read windows size (default 1000000) -mw minimum weight for a call -msw minimum per-sample weight for a call -tt trim threshold -x exclude file bed file -t temp file prefix, must be to a writeable directory -P output probability curve for each variant -b output BEDPE instead of VCF -sr bam_file:<file name>, id:<sample name>, back_distance:<distance>, min_mapping_threshold:<mapping quality>, weight:<sample weight>, min_clip:<minimum clip length>, read_group:<string> -pe bam_file:<file name>, id:<sample name>, histo_file:<file name>, mean:<value>, stdev:<value>, read_length:<length>, min_non_overlap:<length>, discordant_z:<z value>, back_distance:<distance>, min_mapping_threshold:<mapping quality>, weight:<sample weight>, read_group:<string> -bedpe bedpe_file:<bedpe file>, id:<sample name>, weight:<sample weight> </help> <citations> <citation type="doi">10.1186/gb-2014-15-6-r84</citation> </citations> </tool>